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Soto Gomez M, Pokorny L, Kantar MB, Forest F, Leitch IJ, Gravendeel B, Wilkin P, Graham SW, Viruel J. A customized nuclear target enrichment approach for developing a phylogenomic baseline for Dioscorea yams (Dioscoreaceae). APPLICATIONS IN PLANT SCIENCES 2019; 7:e11254. [PMID: 31236313 PMCID: PMC6580989 DOI: 10.1002/aps3.11254] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 04/01/2019] [Indexed: 05/14/2023]
Abstract
PREMISE We developed a target enrichment panel for phylogenomic studies of Dioscorea, an economically important genus with incompletely resolved relationships. METHODS Our bait panel comprises 260 low- to single-copy nuclear genes targeted to work in Dioscorea, assessed here using a preliminary taxon sampling that includes both distantly and closely related taxa, including several yam crops and potential crop wild relatives. We applied coalescent-based and maximum likelihood phylogenomic inference approaches to the pilot taxon set, incorporating new and published transcriptome data from additional species. RESULTS The custom panel retrieved ~94% of targets and >80% of full gene length from 88% and 68% of samples, respectively. It has minimal gene overlap with existing panels designed for angiosperm-wide studies and generally recovers longer and more variable targets. Pilot phylogenomic analyses consistently resolve most deep and recent relationships with strong support across analyses and point to revised relationships between the crop species D. alata and candidate crop wild relatives. DISCUSSION Our customized panel reliably retrieves targeted loci from Dioscorea, is informative for resolving relationships in denser samplings, and is suitable for refining our understanding of the independent origins of cultivated yam species; the panel likely has broader promise for phylogenomic studies across Dioscoreales.
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Affiliation(s)
- Marybel Soto Gomez
- Department of BotanyUniversity of British Columbia6270 University BoulevardVancouverBritish ColumbiaV6T 1Z4Canada
- UBC Botanical Garden and Centre for Plant ResearchUniversity of British Columbia6804 Marine Drive SWVancouverBritish ColumbiaV6T 1Z4Canada
| | - Lisa Pokorny
- Royal Botanic GardensKew, RichmondSurreyTW9 3DSUnited Kingdom
| | - Michael B. Kantar
- Department of Tropical Plant and Soil SciencesUniversity of Hawai‘i at ManoaHonoluluHawai‘i96822USA
| | - Félix Forest
- Royal Botanic GardensKew, RichmondSurreyTW9 3DSUnited Kingdom
| | - Ilia J. Leitch
- Royal Botanic GardensKew, RichmondSurreyTW9 3DSUnited Kingdom
| | - Barbara Gravendeel
- Naturalis Biodiversity CenterEndless FormsSylviusweg 72Leiden2333 BEThe Netherlands
- Institute Biology LeidenLeiden UniversitySylviusweg 72Leiden2333 BEThe Netherlands
- Faculty of Science and TechnologyUniversity of Applied Sciences LeidenZernikedreef 11Leiden2333 CKThe Netherlands
| | - Paul Wilkin
- Royal Botanic GardensKew, RichmondSurreyTW9 3DSUnited Kingdom
| | - Sean W. Graham
- Department of BotanyUniversity of British Columbia6270 University BoulevardVancouverBritish ColumbiaV6T 1Z4Canada
- UBC Botanical Garden and Centre for Plant ResearchUniversity of British Columbia6804 Marine Drive SWVancouverBritish ColumbiaV6T 1Z4Canada
| | - Juan Viruel
- Royal Botanic GardensKew, RichmondSurreyTW9 3DSUnited Kingdom
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Wumbei A, Houbraken M, Spanoghe P. Pesticides use and exposure among yam farmers in the Nanumba traditional area of Ghana. ENVIRONMENTAL MONITORING AND ASSESSMENT 2019; 191:307. [PMID: 31028501 DOI: 10.1007/s10661-019-7449-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 04/04/2019] [Indexed: 06/09/2023]
Abstract
Over the years, pesticides have become a dominant feature of Ghana's agriculture. In the past, pesticides usage was restricted to the cocoa, cotton, vegetables, and fruits sectors. Today, there is a widespread use of pesticides in the cultivation of yam. Since the introduction of pesticides into yam production, farmers have expressed satisfaction about the relief it has brought them with regard to labor and productivity. However, there has been public concern about the human and environmental health impacts of pesticides. In this study, 100 farmers were interviewed through a structured questionnaire to determine their knowledge, awareness, and use practices of pesticides and to determine their level of exposure. The study revealed that the common pesticides currently being used for yam production are herbicides. Although the farmers are aware of the risks associated with the use of pesticides, they use more than the recommended doses and do not pay attention to the use of personal protective equipment (PPE) thereby predisposing themselves to the potential health effects of pesticides. A significant percentage (20 to 40%) of the farmers reported to have never used these PPEs and over 44% of them use glyphosate above the recommended dose (between 1.5 and 2 L/ha). This resulted in an average farmer exposure to glyphosate of 4.2 mg/kgBW/day, well above the acute reference dose (ARfD) of 0.5 mg/kgBW/day. The government should develop and implement programs to train pesticides dealers, educate farmers, enforce the laws on pesticides, and support farmers to uphold protective measures.
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Affiliation(s)
- Abukari Wumbei
- Faculty of Bioscience Engineering, Department of Crops and Plants, Ghent University, Coupure 653, 9000, Ghent, Belgium.
- Institute for Interdisciplinary Research and Consultancy, University for Development Studies, P. O. Box TL 1350, Tamale, Ghana.
| | - Michael Houbraken
- Faculty of Bioscience Engineering, Department of Crops and Plants, Ghent University, Coupure 653, 9000, Ghent, Belgium
| | - Pieter Spanoghe
- Faculty of Bioscience Engineering, Department of Crops and Plants, Ghent University, Coupure 653, 9000, Ghent, Belgium
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53
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Bömer M, Rathnayake AI, Visendi P, Sewe SO, Sicat JPA, Silva G, Kumar PL, Seal SE. Tissue culture and next-generation sequencing: A combined approach for detecting yam ( Dioscorea spp.) viruses. PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY 2019; 105:54-66. [PMID: 31007374 PMCID: PMC6472605 DOI: 10.1016/j.pmpp.2018.06.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 05/04/2018] [Accepted: 06/16/2018] [Indexed: 06/09/2023]
Abstract
In vitro culture offers many advantages for yam germplasm conservation, propagation and international distribution. However, low virus titres in the generated tissues pose a challenge for reliable virus detection, which makes it difficult to ensure that planting material is virus-free. In this study, we evaluated next-generation sequencing (NGS) for virus detection following yam propagation using a robust tissue culture methodology. We detected and assembled the genomes of novel isolates of already characterised viral species of the genera Badnavirus and Potyvirus, confirming the utility of NGS in diagnosing yam viruses and contributing towards the safe distribution of germplasm.
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Affiliation(s)
- Moritz Bömer
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK
| | - Ajith I. Rathnayake
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK
| | - Paul Visendi
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK
| | - Steven O. Sewe
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK
| | - Juan Paolo A. Sicat
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK
| | - Gonçalo Silva
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK
| | - P. Lava Kumar
- International Institute of Tropical Agriculture (IITA), Oyo Road, PMB 5320, Ibadan, Nigeria
| | - Susan E. Seal
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK
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Xue HY, Li JR, Liu YG, Gao Q, Wang XW, Zhang JW, Tanokura M, Xue YL. Optimization of the ultrafiltration-assisted extraction of Chinese yam polysaccharide using response surface methodology and its biological activity. Int J Biol Macromol 2019; 121:1186-1193. [DOI: 10.1016/j.ijbiomac.2018.10.126] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 09/25/2018] [Accepted: 10/15/2018] [Indexed: 11/16/2022]
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Mubaiwa J, Fogliano V, Chidewe C, Bakker EJ, Linnemann AR. Utilization of bambara groundnut (Vigna subterranea (L.) Verdc.) for sustainable food and nutrition security in semi-arid regions of Zimbabwe. PLoS One 2018; 13:e0204817. [PMID: 30278086 PMCID: PMC6168134 DOI: 10.1371/journal.pone.0204817] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 09/15/2018] [Indexed: 11/18/2022] Open
Abstract
Bambara groundnut (Vigna subterranea (L.) Verdc.) is an indigenous legume crop, cultivated by subsistence farmers throughout sub-Saharan countries. Research findings indicate that the crop has great nutritional and agronomic potential, but it remains scientifically neglected. A baseline study was conducted in seven districts in semi-arid regions of rural Zimbabwe to gather knowledge on current production and utilization of bambara groundnut, assess its role in providing sustainable food and nutrition security for rural populations and determine priorities for follow-up research. Results revealed a variety of bambara groundnut processing techniques, which included boiling, soaking, roasting and milling across the surveyed districts. Reported constraints to processing and consumption included long cooking time, difficulties with milling and high firewood and water requirements. Fifty to eighty percent of respondents in all districts consumed bambara groundnut once or twice weekly from August to December. Preferred consumer attributes were taste, the satiating effect, nutritional benefits or a combination of these. Current, culturally acceptable processing techniques need improvement to support sustainable bambara groundnut processing while optimising nutrient bio-accessibility. Ultimately, community resilience to food and nutrition insecurity can be promoted by exchange of bambara groundnut processing knowledge amongst the production areas, involving the different stakeholders in the food supply chains.
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Affiliation(s)
- Juliet Mubaiwa
- Department of Food Science and Technology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
- Food Quality and Design, Wageningen, The Netherlands
| | | | - Cathrine Chidewe
- Department of Biochemistry, University of Zimbabwe, Mount Pleasant, Harare, Zimbabwe
| | - Evert Jan Bakker
- Mathematical and Statistical Methods, Wageningen University, Wageningen, The Netherlands
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Silva G, Oyekanmi J, Nkere CK, Bömer M, Kumar PL, Seal SE. Rapid detection of potyviruses from crude plant extracts. Anal Biochem 2018; 546:17-22. [PMID: 29378167 PMCID: PMC5873530 DOI: 10.1016/j.ab.2018.01.019] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 01/18/2018] [Accepted: 01/21/2018] [Indexed: 11/16/2022]
Abstract
Potyviruses (genus Potyvirus; family Potyviridae) are widely distributed and represent one of the most economically important genera of plant viruses. Therefore, their accurate detection is a key factor in developing efficient control strategies. However, this can sometimes be problematic particularly in plant species containing high amounts of polysaccharides and polyphenols such as yam (Dioscorea spp.). Here, we report the development of a reliable, rapid and cost-effective detection method for the two most important potyviruses infecting yam based on reverse transcription-recombinase polymerase amplification (RT-RPA). The developed method, named 'Direct RT-RPA', detects each target virus directly from plant leaf extracts prepared with a simple and inexpensive extraction method avoiding laborious extraction of high-quality RNA. Direct RT-RPA enables the detection of virus-positive samples in under 30 min at a single low operation temperature (37 °C) without the need for any expensive instrumentation. The Direct RT-RPA tests constitute robust, accurate, sensitive and quick methods for detection of potyviruses from recalcitrant plant species. The minimal sample preparation requirements and the possibility of storing RPA reagents without cold chain storage, allow Direct RT-RPA to be adopted in minimally equipped laboratories and with potential use in plant clinic laboratories and seed certification facilities worldwide.
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Affiliation(s)
- Gonçalo Silva
- Natural Resources Institute, University of Greenwich, Chatham Maritime, Kent, ME4 4TB, UK.
| | - Joshua Oyekanmi
- International Institute of Tropical Agriculture (IITA), Oyo Road, PMB 5320, Ibadan, Nigeria
| | - Chukwuemeka K Nkere
- International Institute of Tropical Agriculture (IITA), Oyo Road, PMB 5320, Ibadan, Nigeria; National Root Crops Research Institute, Km 8 Ikot Ekpene Road, PMB 7006, Umudike, Nigeria
| | - Moritz Bömer
- Natural Resources Institute, University of Greenwich, Chatham Maritime, Kent, ME4 4TB, UK
| | - P Lava Kumar
- International Institute of Tropical Agriculture (IITA), Oyo Road, PMB 5320, Ibadan, Nigeria
| | - Susan E Seal
- Natural Resources Institute, University of Greenwich, Chatham Maritime, Kent, ME4 4TB, UK
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Chromogenic detection of yam mosaic virus by closed-tube reverse transcription loop-mediated isothermal amplification (CT-RT-LAMP). Arch Virol 2018; 163:1057-1061. [PMID: 29308543 PMCID: PMC5854734 DOI: 10.1007/s00705-018-3706-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 12/26/2017] [Indexed: 01/13/2023]
Abstract
A closed-tube reverse transcription loop-mediated isothermal amplification (CT-RT-LAMP) assay was developed for the detection of yam mosaic virus (YMV, genus Potyvirus) infecting yam (Dioscorea spp.). The assay uses a set of six oligonucleotide primers targeting the YMV coat protein region, and the amplification products in YMV-positive samples are visualized by chromogenic detection with SYBR Green I dye. The CT-RT-LAMP assay detected YMV in leaf and tuber tissues of infected plants. The assay is 100 times more sensitive in detecting YMV than standard RT-PCR, while maintaining the same specificity.
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Shi K, Wu X, Ma J, Zhang J, Zhou L, Wang H, Li L. Effects of Planting and Processing Modes on the Degradation of Dithianon and Pyraclostrobin in Chinese Yam (Dioscorea spp.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:10439-10444. [PMID: 29131625 DOI: 10.1021/acs.jafc.7b03916] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The yam (Dioscorea spp.) is widely cultivated in China. The degradation of dithianon and pyraclostrobin in yams with different planting and processing treatments was investigated in this article. An analytical method for two pesticides in yam and yam plant was developed, and recoveries were between 77% and 93%, with relative standard deviations from 0.8% to 7.4%, respectively. On the basis of this method, half-lives for plants grown on stakes versus plants grown without stakes were compared. The results indicated that the half-life for pesticide residues for plants grown on stakes versus plants grown without stakes differed as 6.7 versus 3.1 days for dithianon and 5.4 versus 5.2 days for pyraclostrobin. Dithianon was significantly influenced by planting mode because of its low stability under sunlight. The processing factors of various processing treatments (hot air-drying, vacuum freeze-drying, microwave vacuum-drying, infrared-drying, steaming, and boiling) were all <1, indicating that those processes can reduce residues of two pesticides at different levels. Significant amounts of residues were removed during the boiling treatment, whereas the others showed less effect.
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Affiliation(s)
- Kaiwei Shi
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences , Beijing 100101, China
| | - Xujin Wu
- Henan Academy of Agricultural Sciences/Henan Key Laboratory of Grain Quality and Safety and Testing/Laboratory of Quality Safety Risk Assessment for Agro-products (Zhengzhou), Ministry of Agriculture, Institute of Quality Standard and Testing Technology for Agro-products , Zhengzhou 450002, China
| | - Jingwei Ma
- Henan Academy of Agricultural Sciences/Henan Key Laboratory of Grain Quality and Safety and Testing/Laboratory of Quality Safety Risk Assessment for Agro-products (Zhengzhou), Ministry of Agriculture, Institute of Quality Standard and Testing Technology for Agro-products , Zhengzhou 450002, China
| | - Junfeng Zhang
- Henan Academy of Agricultural Sciences/Henan Key Laboratory of Grain Quality and Safety and Testing/Laboratory of Quality Safety Risk Assessment for Agro-products (Zhengzhou), Ministry of Agriculture, Institute of Quality Standard and Testing Technology for Agro-products , Zhengzhou 450002, China
| | - Ling Zhou
- Henan Academy of Agricultural Sciences/Henan Key Laboratory of Grain Quality and Safety and Testing/Laboratory of Quality Safety Risk Assessment for Agro-products (Zhengzhou), Ministry of Agriculture, Institute of Quality Standard and Testing Technology for Agro-products , Zhengzhou 450002, China
| | - Hong Wang
- Henan Academy of Agricultural Sciences/Henan Key Laboratory of Grain Quality and Safety and Testing/Laboratory of Quality Safety Risk Assessment for Agro-products (Zhengzhou), Ministry of Agriculture, Institute of Quality Standard and Testing Technology for Agro-products , Zhengzhou 450002, China
| | - Li Li
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences , Beijing 100101, China
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Frossard E, Aighewi BA, Aké S, Barjolle D, Baumann P, Bernet T, Dao D, Diby LN, Floquet A, Hgaza VK, Ilboudo LJ, Kiba DI, Mongbo RL, Nacro HB, Nicolay GL, Oka E, Ouattara YF, Pouya N, Senanayake RL, Six J, Traoré OI. The Challenge of Improving Soil Fertility in Yam Cropping Systems of West Africa. FRONTIERS IN PLANT SCIENCE 2017; 8:1953. [PMID: 29209341 PMCID: PMC5702320 DOI: 10.3389/fpls.2017.01953] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 10/30/2017] [Indexed: 05/26/2023]
Abstract
Yam (Dioscorea spp.) is a tuber crop grown for food security, income generation, and traditional medicine. This crop has a high cultural value for some of the groups growing it. Most of the production comes from West Africa where the increased demand has been covered by enlarging cultivated surfaces while the mean yield remained around 10 t tuber ha-1. In West Africa, yam is traditionally cultivated without input as the first crop after a long-term fallow as it is considered to require a high soil fertility. African soils, however, are being more and more degraded. The aims of this review were to show the importance of soil fertility for yam, discuss barriers that might limit the adoption of integrated soil fertility management (ISFM) in yam-based systems in West Africa, present the concept of innovation platforms (IPs) as a tool to foster collaboration between actors for designing innovations in yam-based systems and provide recommendations for future research. This review shows that the development of sustainable, feasible, and acceptable soil management innovations for yam requires research to be conducted in interdisciplinary teams including natural and social sciences and in a transdisciplinary manner involving relevant actors from the problem definition, to the co-design of soil management innovations, the evaluation of research results, their communication and their implementation. Finally, this research should be conducted in diverse biophysical and socio-economic settings to develop generic rules on soil/plant relationships in yam as affected by soil management and on how to adjust the innovation supply to specific contexts.
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Affiliation(s)
- Emmanuel Frossard
- Group of Plant Nutrition, Institute of Agricultural Sciences, ETH Zurich, Lindau, Switzerland
| | - Beatrice A. Aighewi
- Yam Improvement for Income and Food Security in West Africa Project, Research for Development, International Institute for Tropical Agriculture, Abuja, Nigeria
| | - Sévérin Aké
- Laboratory of Plant Physiology, Université Felix Houphouët Boigny, Abidjan, Côte d'Ivoire
| | - Dominique Barjolle
- Group of Sustainable Agroecosystems, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Philipp Baumann
- Group of Sustainable Agroecosystems, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Thomas Bernet
- Department of International Cooperation, Research Institute of Organic Agriculture, Frick, Switzerland
| | - Daouda Dao
- Département Recherche et Développement, Groupe de recherche sécurité alimentaire, Centre Suisse de Recherches Scientifiques, Abidjan, Côte d'Ivoire
| | - Lucien N. Diby
- Côte d'Ivoire Country Programme, World Agroforestry Centre, Abidjan, Côte d'Ivoire
| | - Anne Floquet
- Laboratoire d'Analyse des Dynamiques Sociales et du Développement, Université d'Abomey-Calavi, Cotonou, Benin
| | - Valérie K. Hgaza
- Département Recherche et Développement, Groupe de recherche sécurité alimentaire, Centre Suisse de Recherches Scientifiques, Abidjan, Côte d'Ivoire
| | - Léa J. Ilboudo
- Côte d'Ivoire Country Programme, World Agroforestry Centre, Abidjan, Côte d'Ivoire
| | - Delwende I. Kiba
- Group of Plant Nutrition, Institute of Agricultural Sciences, ETH Zurich, Lindau, Switzerland
- Laboratoire Sol Eau Plante, Institut de l'Environnement et Recherches Agricoles, Ouagadougou, Burkina Faso
| | - Roch L. Mongbo
- Laboratoire d'Analyse des Dynamiques Sociales et du Développement, Université d'Abomey-Calavi, Cotonou, Benin
| | - Hassan B. Nacro
- Laboratoire d'étude et de recherche sur la fertilité du sol, Institut du Développement Rural, Université Nazi Boni, Bobo Dioulasso, Burkina Faso
| | - Gian L. Nicolay
- Department of International Cooperation, Research Institute of Organic Agriculture, Frick, Switzerland
| | - Esther Oka
- Laboratoire d'Analyse des Dynamiques Sociales et du Développement, Université d'Abomey-Calavi, Cotonou, Benin
| | - Yabile F. Ouattara
- Laboratoire d'Analyse des Dynamiques Sociales et du Développement, Université d'Abomey-Calavi, Cotonou, Benin
| | - Nestor Pouya
- Laboratoire d'étude et de recherche sur la fertilité du sol, Institut du Développement Rural, Université Nazi Boni, Bobo Dioulasso, Burkina Faso
| | - Ravinda L. Senanayake
- Group of Plant Nutrition, Institute of Agricultural Sciences, ETH Zurich, Lindau, Switzerland
- Department of Agriculture, Field Crops Research and Development Institute, Mahailluppallama, Sri Lanka
| | - Johan Six
- Group of Sustainable Agroecosystems, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Orokya I. Traoré
- Laboratoire d'étude et de recherche sur la fertilité du sol, Institut du Développement Rural, Université Nazi Boni, Bobo Dioulasso, Burkina Faso
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Bömer M, Rathnayake AI, Visendi P, Silva G, Seal SE. Complete genome sequence of a new member of the genus Badnavirus, Dioscorea bacilliform RT virus 3, reveals the first evidence of recombination in yam badnaviruses. Arch Virol 2017; 163:533-538. [PMID: 29134336 PMCID: PMC5799344 DOI: 10.1007/s00705-017-3605-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 09/27/2017] [Indexed: 11/03/2022]
Abstract
Yams (Dioscorea spp.) host a diverse range of badnaviruses (genus Badnavirus, family Caulimoviridae). The first complete genome sequence of Dioscorea bacilliform RT virus 3 (DBRTV3), which belongs to the monophyletic species group K5, is described. This virus is most closely related to Dioscorea bacilliform SN virus (DBSNV, group K4) based on a comparison of genome sequences. Recombination analysis identified a unique recombination event in DBRTV3, with DBSNV likely to be the major parent and Dioscorea bacilliform AL virus (DBALV) the minor parent, providing the first evidence for recombination in yam badnaviruses. This has important implications for yam breeding programmes globally.
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Affiliation(s)
- Moritz Bömer
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK.
| | - Ajith I Rathnayake
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK
| | - Paul Visendi
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK
| | - Gonçalo Silva
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK
| | - Susan E Seal
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK
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PCR-DGGE Analysis: Unravelling Complex Mixtures of Badnavirus Sequences Present in Yam Germplasm. Viruses 2017; 9:v9070181. [PMID: 28696406 PMCID: PMC5537673 DOI: 10.3390/v9070181] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 06/29/2017] [Accepted: 07/04/2017] [Indexed: 12/19/2022] Open
Abstract
Badnaviruses (family Caulimoviridae, genus Badnavirus) have emerged as serious pathogens especially affecting the cultivation of tropical crops. Badnavirus sequences can be integrated in host genomes, complicating the detection of episomal infections and the assessment of viral genetic diversity in samples containing a complex mixture of sequences. Yam (Dioscorea spp.) plants are hosts to a diverse range of badnavirus species, and recent findings have suggested that mixed infections occur frequently in West African yam germplasm. Historically, the determination of the diversity of badnaviruses present in yam breeding lines has been achieved by cloning and sequencing of polymerase chain reaction (PCR) products. In this study, the molecular diversity of partial reverse transcriptase (RT)-ribonuclease H (RNaseH) sequences from yam badnaviruses was analysed using PCR-dependent denaturing gradient gel electrophoresis (PCR-DGGE). This resulted in the identification of complex ‘fingerprints’ composed of multiple sequences of Dioscorea bacilliform viruses (DBVs). Many of these sequences show high nucleotide identities to endogenous DBV (eDBV) sequences deposited in GenBank, and fall into six monophyletic species groups. Our findings highlight PCR-DGGE as a powerful tool in badnavirus diversity studies enabling a rapid indication of sequence diversity as well as potential candidate integrated sequences revealed by their conserved nature across germplasm.
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62
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Price EJ, Bhattacharjee R, Lopez-Montes A, Fraser PD. Metabolite profiling of yam ( Dioscorea spp.) accessions for use in crop improvement programmes. Metabolomics 2017; 13:144. [PMID: 29104519 PMCID: PMC5641283 DOI: 10.1007/s11306-017-1279-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 09/22/2017] [Indexed: 01/30/2023]
Abstract
INTRODUCTION Ninety-seven percent of yam (Dioscorea spp.) production takes place in low income food deficit countries (LIFDCs) and the crop provides 200 calories a day to approximately 300 million people. Therefore, yams are vital for food security. Yams have high-yield potential and high market value potential yet current breeding of yam is hindered by a lack of genomic information and genetic resources. New tools are needed to modernise breeding strategies and unlock the potential of yam to improve livelihood in LIFDCs. OBJECTIVES Metabolomic screening has been undertaken on a diverse panel of Dioscorea accessions to assess the utility of the approach for advancing breeding strategies in this understudied crop. METHODS Polar and lipophilic extracts from tubers of accessions from the global yam breeding program have been comprehensively profiled via gas chromatography-mass spectrometry. RESULTS A visual pathway representation of the measured yam tuber metabolome has been delivered as a resource for biochemical evaluation of yam germplasm. Over 200 compounds were routinely measured in tubers, providing a major advance for the chemo-typing of this crop. Core biochemical redundancy concealed trends that were only elucidated following detailed mining of global metabolomics data. Combined analysis on leaf and tuber material identified a subset of metabolites which allow accurate species classification and highlighted the potential of predicting tuber composition from leaf profiles. Metabolic variation was accession-specific and often localised to compound classes, which will aid trait-targeting for metabolite markers. CONCLUSIONS Metabolomics provides a standalone platform with potential to deliver near-future crop gains for yam. The approach compliments the genetic advancements currently underway and integration with other '-omics' studies will deliver a significant advancement to yam breeding strategies.
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Affiliation(s)
- Elliott J. Price
- Royal Holloway University of London, Egham, Surrey, TW20 0EX UK
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW20 3AB UK
| | | | - Antonio Lopez-Montes
- International Institute of Tropical Agriculture, Oyo Road, PMB 5320 Ibadan, Nigeria
| | - Paul D. Fraser
- Royal Holloway University of London, Egham, Surrey, TW20 0EX UK
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Kolombia YA, Karssen G, Viaene N, Kumar PL, Joos L, Coyne DL, Bert W. Morphological and molecular characterisation of Scutellonema species from yam ( Dioscorea spp.) and a key to the species of the genus. NEMATOLOGY 2017; 19:751-787. [PMID: 32704234 PMCID: PMC7340491 DOI: 10.1163/15685411-00003084] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 05/30/2017] [Accepted: 06/01/2017] [Indexed: 11/24/2022]
Abstract
The yam nematode, Scutellonema bradys, is a major threat to yam (Dioscorea spp.) production across yam-growing regions. In West Africa, this species cohabits with many morphologically similar congeners and, consequently, its accurate diagnosis is essential for control and for monitoring its movement. In the present study, 46 Scutellonema populations collected from yam rhizosphere and yam tubers in different agro-ecological zones in Ghana and Nigeria were characterised by their morphological features and by sequencing of the D2-D3 region of the 28S rDNA gene and the mitochondrial COI genes. Molecular phylogeny, molecular species delimitation and morphology revealed S. bradys, S. cavenessi, S. clathricaudatum and three undescribed species from yam rhizosphere. Only S. bradys was identified from yam tuber tissue, however. For barcoding and identifying Scutellonema spp., the most suitable marker used was the COI gene. Additionally, 99 new Scutellonema sequences were generated using populations obtained also from banana, carrot, maize and tomato, including the first for S. paralabiatum and S. clathricaudatum, enabling the development of a dichotomous key for identification of Scutellonema spp. The implications of these results are discussed.
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Affiliation(s)
- Yao A Kolombia
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.,International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Road, Ibadan, Nigeria
| | - Gerrit Karssen
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.,National Plant Protection Organization, 6706 EA Wageningen, The Netherlands
| | - Nicole Viaene
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.,Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), B-9820 Merelbeke, Belgium
| | - P Lava Kumar
- International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Road, Ibadan, Nigeria
| | - Lisa Joos
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Danny L Coyne
- IITA, Kasarani, P.O. Box 30772-00100, Nairobi, Kenya
| | - Wim Bert
- Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
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64
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The role of wild edible plants in household food security among transitioning hunter-gatherers: evidence from the Philippines. Food Secur 2016. [DOI: 10.1007/s12571-016-0630-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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65
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Maurin O, Muasya AM, Catalan P, Shongwe EZ, Viruel J, Wilkin P, van der Bank M. Diversification into novel habitats in the Africa clade of Dioscorea (Dioscoreaceae): erect habit and elephant's foot tubers. BMC Evol Biol 2016; 16:238. [PMID: 27821045 PMCID: PMC5100304 DOI: 10.1186/s12862-016-0812-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 10/25/2016] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Dioscorea is a widely distributed and highly diversified genus in tropical regions where it is represented by ten main clades, one of which diversified exclusively in Africa. In southern Africa it is characterised by a distinct group of species with a pachycaul or "elephant's foot" structure that is partially to fully exposed above the substrate. In contrast to African representatives of the genus from other clades, occurring mainly in forest or woodland, the pachycaul taxa and their southern African relatives occur in diverse habitats ranging from woodland to open vegetation. Here we investigate patterns of diversification in the African clade, time of transition from forest to more open habitat, and morphological traits associated with each habitat and evaluate if such transitions have led to modification of reproductive organs and mode of dispersal. RESULTS The Africa clade originated in the Oligocene and comprises four subclades. The Dioscorea buchananii subclade (southeastern tropical Africa and South Africa) is sister to the East African subclade, which is respectively sister to the recently evolved sister South African (e. g., Cape and Pachycaul) subclades. The Cape and Pachycaul subclades diversified in the east of the Cape Peninsula in the mid Miocene, in an area with complex geomorphology and climate, where the fynbos, thicket, succulent karoo and forest biomes meet. CONCLUSIONS Diversification out of forest is associated with major shifts in morphology of the perennial tuber (specifically an increase in size and orientation which presumably led them to become pachycaul) and rotation of stem (from twining to non-twining). The iconic elephant's foot morphology, observed in grasslands and thicket biomes, where its corky bark may offer protection against fire and herbivory, evolved since mid Miocene. A shift in pollination trait is observed within the forest, but entry into open habitat does not show association with reproductive morphology, except in the seed wing, which has switched from winged all round the seed margin to just at the base or at the apex of it, or has been even replaced by an elaiosome.
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Affiliation(s)
- Olivier Maurin
- African Centre for DNA Barcoding, Department of Botany & Plant Biotechnology, University of Johannesburg, PO Box 524, Auckland Park, Johannesburg, Gauteng, 2006, South Africa
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - A Muthama Muasya
- Department of Biological Sciences, University of Cape Town, Rondebosch, Western Cape, 7701, South Africa.
| | - Pilar Catalan
- Departamento de Ciencias Agrarias y del Medio Natural, Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Ctra. Cuarte km 1, Huesca, 22071, Spain
- Institute of Biology, Tomsk State University, 36 Lenin Avenue, Tomsk, 634050, Russia
| | - Eugene Z Shongwe
- African Centre for DNA Barcoding, Department of Botany & Plant Biotechnology, University of Johannesburg, PO Box 524, Auckland Park, Johannesburg, Gauteng, 2006, South Africa
| | - Juan Viruel
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Av. Reina Mercedes s/n, Sevilla, 41012, Spain
- Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale (IMBE), Aix Marseille Université, Chemin de la Batterie des Lions, Marseille, 13007, France
| | - Paul Wilkin
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Michelle van der Bank
- African Centre for DNA Barcoding, Department of Botany & Plant Biotechnology, University of Johannesburg, PO Box 524, Auckland Park, Johannesburg, Gauteng, 2006, South Africa
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Bömer M, Turaki AA, Silva G, Kumar PL, Seal SE. A Sequence-Independent Strategy for Amplification and Characterisation of Episomal Badnavirus Sequences Reveals Three Previously Uncharacterised Yam Badnaviruses. Viruses 2016; 8:E188. [PMID: 27399761 PMCID: PMC4974523 DOI: 10.3390/v8070188] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 06/24/2016] [Accepted: 06/30/2016] [Indexed: 12/17/2022] Open
Abstract
Yam (Dioscorea spp.) plants are potentially hosts to a diverse range of badnavirus species (genus Badnavirus, family Caulimoviridae), but their detection is complicated by the existence of integrated badnavirus sequences in some yam genomes. To date, only two badnavirus genomes have been characterised, namely, Dioscorea bacilliform AL virus (DBALV) and Dioscorea bacilliform SN virus (DBSNV). A further 10 tentative species in yam have been described based on their partial reverse transcriptase (RT)-ribonuclease H (RNaseH) sequences, generically referred to here as Dioscorea bacilliform viruses (DBVs). Further characterisation of DBV species is necessary to determine which represent episomal viruses and which are only present as integrated badnavirus sequences in some yam genomes. In this study, a sequence-independent multiply-primed rolling circle amplification (RCA) method was evaluated for selective amplification of episomal DBV genomes. This resulted in the identification and characterisation of nine complete genomic sequences (7.4-7.7 kbp) of existing and previously undescribed DBV phylogenetic groups from Dioscorea alata and Dioscorea rotundata accessions. These new yam badnavirus genomes expand our understanding of the diversity and genomic organisation of DBVs, and assist the development of improved diagnostic tools. Our findings also suggest that mixed badnavirus infections occur relatively often in West African yam germplasm.
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Affiliation(s)
- Moritz Bömer
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham, Kent ME4 4TB, UK.
| | - Aliyu A Turaki
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham, Kent ME4 4TB, UK.
| | - Gonçalo Silva
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham, Kent ME4 4TB, UK.
| | - P Lava Kumar
- International Institute of Tropical Agriculture (IITA), Oyo Road, PMB 5320, Ibadan, Nigeria.
| | - Susan E Seal
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham, Kent ME4 4TB, UK.
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67
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Price EJ, Wilkin P, Sarasan V, Fraser PD. Metabolite profiling of Dioscorea (yam) species reveals underutilised biodiversity and renewable sources for high-value compounds. Sci Rep 2016; 6:29136. [PMID: 27385275 PMCID: PMC4935876 DOI: 10.1038/srep29136] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 06/15/2016] [Indexed: 11/24/2022] Open
Abstract
Yams (Dioscorea spp.) are a multispecies crop with production in over 50 countries generating ~50 MT of edible tubers annually. The long-term storage potential of these tubers is vital for food security in developing countries. Furthermore, many species are important sources of pharmaceutical precursors. Despite these attributes as staple food crops and sources of high-value chemicals, Dioscorea spp. remain largely neglected in comparison to other staple tuber crops of tropical agricultural systems such as cassava (Manihot esculenta) and sweet potato (Ipomoea batatas). To date, studies have focussed on the tubers or rhizomes of Dioscorea, neglecting the foliage as waste. In the present study metabolite profiling procedures, using GC-MS approaches, have been established to assess biochemical diversity across species. The robustness of the procedures was shown using material from the phylogenetic clades. The resultant data allowed separation of the genotypes into clades, species and morphological traits with a putative geographical origin. Additionally, we show the potential of foliage material as a renewable source of high-value compounds.
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Affiliation(s)
- Elliott J. Price
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW20 3AB, UK
| | - Paul Wilkin
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW20 3AB, UK
| | | | - Paul D. Fraser
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
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68
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Barlagne C, Cornet D, Blazy JM, Diman JL, Ozier-Lafontaine H. Consumers' preferences for fresh yam: a focus group study. Food Sci Nutr 2016; 5:54-66. [PMID: 28070316 PMCID: PMC5217904 DOI: 10.1002/fsn3.364] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 03/07/2016] [Accepted: 03/08/2016] [Indexed: 11/10/2022] Open
Abstract
In West and Central Africa and in the Caribbean, yam is one of the most important sources of carbohydrates and has a great potential to improve food security. The yam production sector is, however, now challenged by the satisfaction of evolving consumers' preferences. Since little is known about consumers' preferences regarding yams' characteristics, product quality, and the drivers of yam purchase, six focus group discussions were conducted (for a total of 31 participants). Among the purchasing criteria, price was considered more important than the others. It was followed by the external damage, the origin, and the size of the tuber. The most frequently cited consumption criteria were the taste, the texture, and color of flesh after cooking. Taste was considered more important than the other criteria. Three consumers' profiles were established reflecting heterogeneity in preferences, especially as concerns the willingness to pay for yam and consumption habits. They were designated as the Hedonistic, the Thrifty and the Flexible. Our results suggest that innovations can be implemented to sustain and stimulate the development of the yam sector in Guadeloupe. Two main development paths were identified. The first path is the valorization of the great existing diversity of yam varieties and the increase in the level of information for consumers about product attributes such as the cooking mode, the origin, and the mode of production. Building a marketing strategy based on the valorization of this diversity can help maintain and preserve yam's agro‐biodiversity and the satisfaction of rapidly evolving consumption habits. The second path is the definition of yam ideotypes that suit consumers' needs. We expect that tailoring the production to consumers' needs will have a positive impact on global food security in the Caribbean region.
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Affiliation(s)
- Carla Barlagne
- UR1321 ASTRO Agrosystèmes tropicaux INRA Petit-Bourg (Guadeloupe) F-97170 France
| | - Denis Cornet
- UMR AGAP CIRAD Petit-Bourg (Guadeloupe) F-97170 France
| | - Jean-Marc Blazy
- UR1321 ASTRO Agrosystèmes tropicaux INRA Petit-Bourg (Guadeloupe) F-97170 France
| | - Jean-Louis Diman
- UR1321 ASTRO Agrosystèmes tropicaux INRA Petit-Bourg (Guadeloupe) F-97170 France
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69
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Silva G, Bömer M, Nkere C, Lava Kumar P, Seal SE. Rapid and specific detection of Yam mosaic virus by reverse-transcription recombinase polymerase amplification. J Virol Methods 2015; 222:138-44. [DOI: 10.1016/j.jviromet.2015.06.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 06/16/2015] [Accepted: 06/20/2015] [Indexed: 12/21/2022]
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Complete genome sequence of a divergent strain of Japanese yam mosaic virus from China. Arch Virol 2014; 160:573-6. [PMID: 25244960 DOI: 10.1007/s00705-014-2231-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 09/08/2014] [Indexed: 10/24/2022]
Abstract
A novel strain of Japanese yam mosaic virus (JYMV-CN) was identified in a yam plant with foliar mottle symptoms in China. The complete genomic sequence of JYMV-CN was determined. Its genomic sequence of 9701 nucleotides encodes a polyprotein of 3247 amino acids. Its organization is virtually identical to that of two JYMV isolates from Japan. With the latter, it shares nucleotide sequence identities of only 74.7-74.8 %, indicating it might be a member of a new species. However, sequence analysis of the polyprotein and individual proteins suggested that the Chinese isolate is a divergent JYMV strain in the process of speciation.
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71
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Velasco-Ramírez AP, Torres-Morán MI, Molina-Moret S, Sánchez-González JDJ, Santacruz-Ruvalcaba F. Efficiency of RAPD, ISSR, AFLP and ISTR markers for the detection of polymorphisms and genetic relationships in camote de cerro (Dioscorea spp.). ELECTRON J BIOTECHN 2014. [DOI: 10.1016/j.ejbt.2014.01.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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72
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Seal S, Turaki A, Muller E, Kumar PL, Kenyon L, Filloux D, Galzi S, Lopez-Montes A, Iskra-Caruana ML. The prevalence of badnaviruses in West African yams (Dioscorea cayenensis-rotundata) and evidence of endogenous pararetrovirus sequences in their genomes. Virus Res 2014; 186:144-54. [PMID: 24457074 DOI: 10.1016/j.virusres.2014.01.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 12/19/2013] [Accepted: 01/11/2014] [Indexed: 02/09/2023]
Abstract
Yam (Dioscorea spp.) is an important vegetatively-propagated staple crop in West Africa. Viruses are pervasive in yam worldwide, decreasing growth and yield, as well as hindering the international movement of germplasm. Badnaviruses have been reported to be the most prevalent in yam, and genomes of some other badnaviruses are known to be integrated in their host plant species. However, it was not clear if a similar scenario occurs in Dioscorea yam. This study was conducted to verify the prevalence of badnaviruses, and determine if badnavirus genomes are integrated in the yam genome. Leaf samples (n=58) representing eight species of yam from global yam collections kept at CIRAD, France, and 127 samples of D. rotundata breeding lines (n=112) and landraces (n=15) at IITA, Nigeria, were screened using generic badnavirus PCR primers. Positive amplification of an expected ca. 579bp fragment, corresponding to a partial RT-RNaseH region, was detected in 47 (81%) of 58 samples analysed from CIRAD collections, and 100% of the 127 IITA D. rotundata samples. All the D. cayenensis and D. rotundata samples from the CIRAD and IITA collections tested PCR-positive, and sequencing of a selection of the PCR products confirmed they were typical of the genus Badnavirus. A comparison of serological and nucleic acid techniques was used to investigate whether the PCR-positives were sequences amplified from badnavirus particles or putative endogenous badnavirus sequences in the yam genome. Protein A sandwich-enzyme-linked immunosorbent assay (PAS-ELISA) with badnavirus polyclonal antisera detected cross-reacting viral particles in only 60% (92 of 153) of the CIRAD collection samples analysed, in contrast to the aforementioned 81% by PCR. Immunosorbent electron microscopy (ISEM) of virus preparations of a select set of 16 samples, representing different combinations of positive and negative PCR and PAS-ELISA results, identified bacilliform particles in 11 of these samples. Three PCR-positive yam samples from Burkina Faso (cv. Pilimpikou) were identified in which no viral particles were detected by either PAS-ELISA or ISEM. Southern hybridisation results using a yam badnavirus RT-RNaseH sequence (Gn155Dr) as probe, supported a lack of badnavirus particles in the cv. Pilimpikou and identified their equivalent sequences to be of plant genome origin. Probe Gn155Dr, however, hybridised to viral particles and plant genomic DNA in three D. rotundata samples from Guinea. These results represent the first data demonstrating the presence of integrated sequences of badnaviruses in yam. The implications of this for virus-indexing, breeding and multiplication of seed yams are discussed.
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Affiliation(s)
- Susan Seal
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK; CIRAD, UMR BGPI, F-34098 Montpellier, France.
| | - Aliyu Turaki
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK
| | | | - P Lava Kumar
- International Institute of Tropical Agriculture (IITA), Oyo Road PMB 5320, Ibadan, Nigeria
| | - Lawrence Kenyon
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK
| | | | - Serge Galzi
- CIRAD, UMR BGPI, F-34098 Montpellier, France
| | - Antonio Lopez-Montes
- International Institute of Tropical Agriculture (IITA), Oyo Road PMB 5320, Ibadan, Nigeria
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Graham-Acquaah S, Ayernor G, Bediako-Amoa B, Saalia F, Afoakwa E, Abbey L. Effect of Blanching and Frying on Textural Profile and Appearance of Yam (D
ioscorea rotundata
) French Fries. J FOOD PROCESS PRES 2013. [DOI: 10.1111/jfpp.12204] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- S. Graham-Acquaah
- Department of Nutrition and Food Science; University of Ghana; Accra Ghana
| | - G.S. Ayernor
- Department of Nutrition and Food Science; University of Ghana; Accra Ghana
| | - B. Bediako-Amoa
- Department of Nutrition and Food Science; University of Ghana; Accra Ghana
| | - F.S. Saalia
- Department of Nutrition and Food Science; University of Ghana; Accra Ghana
| | - E.O. Afoakwa
- Department of Nutrition and Food Science; University of Ghana; Accra Ghana
| | - L. Abbey
- Food Research Institute; Accra Ghana
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A new source of elemol rich essential oil and existence of multicellular oil glands in leaves of the Dioscorea species. ScientificWorldJournal 2013; 2013:943598. [PMID: 24453926 PMCID: PMC3884965 DOI: 10.1155/2013/943598] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 10/01/2013] [Indexed: 11/17/2022] Open
Abstract
Dioscorea species is a very important food and drug plant. The tubers of the plant are extensively used in food and drug purposes owing to the presence of steroidal constituent's diosgenin in the tubers. In the present study, we report for the first time that the leaves of Dioscorea composita and Dioscorea floribunda grown under the field conditions exhibited the presence of multicellular oil glands on the epidermal layers of the plants using stereomicroscopy (SM) and scanning electron microscopy (SEM). Essential oil was also isolated from the otherwise not useful herbage of the plant, and gas chromatographic-mass spectroscopy analysis revealed confirmation of the essential oil constituents. Out of the 76 compounds detected in D. floribunda and 37 from D. composita essential oil, major terpenoids which are detected and reported for Dioscorea leaf essential oil are α-terpinene, nerolidol, citronellyl acetate, farnesol, elemol, α-farnesene, valerenyl acetate, and so forth. Elemol was detected as the major constituent of both the Dioscorea species occupying 41% and 22% of D. Floribunda and D. composita essential oils, respectively. In this paper, we report for the first time Dioscorea as a possible novel bioresource for the essential oil besides its well-known importance for yielding diosgenin.
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Seth D, Badwaik LS, Ganapathy V. Effect of feed composition, moisture content and extrusion temperature on extrudate characteristics of yam-corn-rice based snack food. Journal of Food Science and Technology 2013; 52:1830-8. [PMID: 25745265 DOI: 10.1007/s13197-013-1181-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 09/09/2013] [Accepted: 09/26/2013] [Indexed: 11/25/2022]
Abstract
Blends of yam, rice and corn flour were processed in a twin-screw extruder. Effects of yam flour (10-40 %), feed moisture content (12-24 %) and extruder barrel temperature (100-140 °C) on the characteristics of the dried extrudates was investigated using a statistical technique response surface methodology (RSM). Radial expansion ratio differed significantly (p ≤ 0.05) with change in all the independent variables. Highest expansion (3.97) was found at lowest moisture content (12 %) and highest barrel temperature (140 °C). Increased yam flour level decreased the expansion ratio significantly. Water absorption index (WAI) increased significantly with increase of all variables. However, water solubility index (WSI) did not change with change in yam flour percent. Hardness of extrudates that varied from 3.86 to 6.94 N was positively correlated with yam flour level and feed moisture content, however it decreased significantly (p ≤ 0.001) with increase of barrel temperature. Yam percent of 15.75 with feed moisture and barrel temperature at 12.00 % and 140 °C respectively gave an optimized product of high desirability (> 0.90) with optimum responses of 3.29 expansion ratio, 5.64 g/g dry solid water absorption index, 30.39 % water solubility index and 3.86 N hardness. The predicted values registered non-significant (p < 0.10) differences from the experimental results. Further study would include the sensory properties enhancement of extruded snacks and little emphasis on the chemistry of interaction between different components.
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Affiliation(s)
- Dibyakanta Seth
- Department of Food Engineering and Technology, Tezpur University, Napam, Tezpur, Assam 784028 India
| | - Laxmikant S Badwaik
- Department of Food Engineering and Technology, Tezpur University, Napam, Tezpur, Assam 784028 India
| | - Vijayalakshmi Ganapathy
- Department of Food Processing and Engineering, Karunya University, Coimbatore, Tamil Nadu 641114 India
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de Lourdes Contreras-Pacheco M, Santacruz-Ruvalcaba F, García-Fajardo JA, de Jesús Sánchez G. J, Ruíz L. MA, Estarrón-Espinosa M, Castro-Castro A. Diosgenin quantification, characterisation and chemical composition in a tuber collection of Dioscoreaspp. in the state of Jalisco, Mexico. Int J Food Sci Technol 2013. [DOI: 10.1111/ijfs.12193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- María de Lourdes Contreras-Pacheco
- Centro Universitario de Ciencias Biológicas y Agropecuarias; Universidad de Guadalajara; Km 15.5, Carretera Guadalajara-Nogales; Las Agujas; Zapopan; Jalisco; C.P. 45110; México
| | - Fernando Santacruz-Ruvalcaba
- Centro Universitario de Ciencias Biológicas y Agropecuarias; Universidad de Guadalajara; Km 15.5, Carretera Guadalajara-Nogales; Las Agujas; Zapopan; Jalisco; C.P. 45110; México
| | - Jorge A. García-Fajardo
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco; A.C. Av. Normalistas No. 800; Colinas de la Normal; Guadalajara; Jalisco; C.P. 44270; México
| | - José de Jesús Sánchez G.
- Centro Universitario de Ciencias Biológicas y Agropecuarias; Universidad de Guadalajara; Km 15.5, Carretera Guadalajara-Nogales; Las Agujas; Zapopan; Jalisco; C.P. 45110; México
| | - Mario A. Ruíz L.
- Centro Universitario de Ciencias Biológicas y Agropecuarias; Universidad de Guadalajara; Km 15.5, Carretera Guadalajara-Nogales; Las Agujas; Zapopan; Jalisco; C.P. 45110; México
| | - Mirna Estarrón-Espinosa
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco; A.C. Av. Normalistas No. 800; Colinas de la Normal; Guadalajara; Jalisco; C.P. 44270; México
| | - Arturo Castro-Castro
- Centro Universitario de Ciencias Biológicas y Agropecuarias; Universidad de Guadalajara; Km 15.5, Carretera Guadalajara-Nogales; Las Agujas; Zapopan; Jalisco; C.P. 45110; México
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Lebot V, Malapa R. Application of near infrared reflectance spectroscopy for the evaluation of yam (Dioscorea alata) germplasm and breeding lines. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2013; 93:1788-1797. [PMID: 23255261 DOI: 10.1002/jsfa.6002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 10/18/2012] [Accepted: 11/20/2012] [Indexed: 06/01/2023]
Abstract
BACKGROUND Thousands of yam (Dioscorea spp.) accessions are maintained in germplasm collections. The physico-chemical characteristics of the tubers are rarely characterised. Unless a simple, low cost, screening tool is available, it is difficult to evaluate the quality of varieties and breeding lines. We investigated the potential of near infrared reflectance spectroscopy (NIRS) as an alternative method for predicting the major constituents of the yam tuber. RESULTS Two hundred and sixty-five accessions, belonging to seven different Dioscorea spp., were analysed for starch, amylose, sugars, proteins, minerals and cellulose. The comparison of the NIR spectra and the chemical values allowed the establishment of equations of calibration for the prediction of starch, sugars and proteins (equivalent N). The r(2) pred values for starch, sugars and proteins (respectively 0.84, 0.86 and 0.88) are high enough to allow good estimates of their contents. Values for the ratio of performance to deviation (RPD) of 4.046 and 3.641 for the sugars and proteins models also allow good quantitative predictions to be made. Amylose, cellulose and minerals could not be predicted precisely. A second calibration conducted by adding the calibration and validation sets (260 accessions) revealed an improvement of the RPD values for starch, sugars and proteins, indicating that the models can be improved. Discriminant analysis conducted using 2151 wavelengths (in nanometres) as variables was applied to a set of 214 accessions of D. alata and the results were compared to the principal component analysis of chemical data. Accessions can be classified according to the amylaceous fraction of the chemotype. CONCLUSION NIRS could be used in yam breeding programmes to characterise rapidly and at low cost the numerous accessions and breeding lines.
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Affiliation(s)
- Vincent Lebot
- Centre International de Recherches Agronomiques pour le Développement, PO Box 946, Port-Vila, Vanuatu.
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Graham-Acquaah S, Ayernor GS, Bediako-Amoa B, Saalia FK, Afoakwa EO. Spatial distribution of total phenolic content, enzymatic activities and browning in white yam (Dioscorea rotundata) tubers. Journal of Food Science and Technology 2012; 51:2833-8. [PMID: 25328234 DOI: 10.1007/s13197-012-0760-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 05/04/2012] [Accepted: 06/11/2012] [Indexed: 11/30/2022]
Abstract
Browning in raw and processed yams resulting from enzymes, polyphenol oxidase (PPO) and peroxidase (POD), activities is a major limitation to the industrial utilization of Dioscorea varieties of yams. Two elite cultivars of D. rotundata species were selected to study the spatial distribution of total phenols and enzymes (PPO and POD) activities. The intensities of tissue darkening in fresh yam chips prepared from the tuber sections of cultivars during frozen storage were also studied. Total phenolic content was observed to be highest in the head and mid sections of the cultivars than at the tail end. PPO activity did not have any specific distribution pattern whereas POD activity was found to be more concentrated in the head than in the middle and tail regions. Browning was found to be most intense in the head regions of the two cultivars studied; and was observed to correlate with total phenol and dry matter contents of tubers. Between the two enzymes, POD activity appeared to be more related to browning than PPO.
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Affiliation(s)
- Seth Graham-Acquaah
- Department of Nutrition and Food Science, University of Ghana, Legon Accra, Ghana
| | - George Sodah Ayernor
- Department of Nutrition and Food Science, University of Ghana, Legon Accra, Ghana
| | - Betty Bediako-Amoa
- Department of Nutrition and Food Science, University of Ghana, Legon Accra, Ghana
| | - Firibu Kwesi Saalia
- Department of Nutrition and Food Science, University of Ghana, Legon Accra, Ghana
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Chiu HW, Peng JC, Tsai SJ, Tsay JR, Lui WB. Process Optimization by Response Surface Methodology and Characteristics Investigation of Corn Extrudate Fortified with Yam (Dioscorea alata L.). FOOD BIOPROCESS TECH 2012. [DOI: 10.1007/s11947-012-0894-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Challinor VL, Smith DM, De Voss JJ. Steroidal Saponins Isolated from an Australian Yam Dioscorea sp. Aust J Chem 2011. [DOI: 10.1071/ch11056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Phytochemical characterization of the rhizome of an Australian species of Dioscorea, acquired as Dioscorea transversa R Br. but botanically identified as Dioscorea sp., led to the isolation of two steroidal saponins. The major constituent 1β-hydroxyprotogracillin (1) was previously unknown while the minor one was identified as protogracillin (2). The structure and stereochemistry of 1 were elucidated using a combination of MS studies, 1D and 2D NMR experiments and chemical degradation.
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